isoCounts: Create count matrix with different summarizing options

View source: R/isomiRs.R

isoCountsR Documentation

Create count matrix with different summarizing options

Description

This function collapses isomiRs into different groups. It is a similar concept than how to work with gene isoforms. With this function, different changes can be put together into a single miRNA variant. For instance all sequences with variants at 3' end can be considered as different elements in the table or analysis having the following naming ⁠hsa-miR-124a-5p.iso.t3:AAA⁠.

Usage

isoCounts(
  ids,
  ref = FALSE,
  iso5 = FALSE,
  iso3 = FALSE,
  add = FALSE,
  snv = FALSE,
  seed = FALSE,
  all = FALSE,
  minc = 1,
  mins = 1,
  merge_by = NULL
)

Arguments

ids

Object of class IsomirDataSeq.

ref

Differentiate reference miRNA from rest.

iso5

Differentiate trimming at 5 miRNA from rest.

iso3

Differentiate trimming at 3 miRNA from rest.

add

Differentiate additions miRNA from rest.

snv

Differentiate nt substitution miRNA from rest.

seed

Differentiate changes in 2-7 nts from rest.

all

Differentiate all isomiRs.

minc

Int minimum number of isomiR sequences to be included.

mins

Int minimum number of samples with number of sequences bigger than minc counts.

merge_by

Column in coldata to merge samples into a single column in counts. Useful to combine technical replicates.

Details

You can merge all isomiRs into miRNAs by calling the function only with the first parameter isoCounts(ids). You can get a table with isomiRs altogether and the reference miRBase sequences by calling the function with ref=TRUE. You can get a table with 5' trimming isomiRS, miRBase reference and the rest by calling with isoCounts(ids, ref=TRUE, iso5=TRUE). If you set up all parameters to TRUE, you will get a table for each different sequence mapping to a miRNA (i.e. all isomiRs).

Examples for the naming used for the isomiRs are at http://seqcluster.readthedocs.org/mirna_annotation.html#mirna-annotation.

Value

IsomirDataSeq object with new count table. The count matrix can be access with counts(ids).

Examples

data(mirData)
ids <- isoCounts(mirData, ref=TRUE)
head(counts(ids))
# taking into account isomiRs and reference sequence.
ids <- isoCounts(mirData, ref=TRUE, minc=10, mins=6)
head(counts(ids))

lpantano/isomiRs documentation built on Aug. 26, 2024, 3:34 a.m.